Locus 1919

Sequence ID	X_DroMel_CAF1
Location	5,293,815 – 5,293,935
Length	120
Max. P	0.903081

overview

Window 1

Location	5,293,815 – 5,293,935
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	78.57
Mean single sequence MFE	-26.73
Consensus MFE	-17.24
Energy contribution	-17.90
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.64
SVM decision value	0.49
SVM RNA-class probability	0.758422
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5293815 120 + 22224390
AAUCCGGUGACCUUGCACCUUCCAGUUUAGCAGUGUGCCAAGCCCACCUCCUGCACCUCAUUGAAUCCAUUGAAUGGAAUGCGACCCCUUUUCUUUUUUCUAUUUUUUUUCUGGGUUUUU
(((((((((..(((((((((.(.......).)).))).))))..))))...((((..(((((.((....)).)))))..)))).............................)))))... ( -23.10)
>DroSec_CAF1 30964 94 + 1
AAUCCGGUGACCUUGCACA---CUGUGUACCAGUGUGCCA-GCCCACCGC---CACCUCAUUGAACCCAUUGAAUGGAAUGCGACCCCUUUU-------------------UCGGGUUCC
....(((((..((.(((((---(((.....)))))))).)-)..))))).---.........((((((...(((.((........)).))).-------------------..)))))). ( -33.60)
>DroSim_CAF1 21748 96 + 1
AAUCCGGUGACCUUGCACCU-CCAGUGUACCAGUGUGCCA-GCCCACCGC---CACCUCAUUGAACCCAUUGAAUGGAAUGCGACCCCUUUU-------------------UCGGGUUUC
....(((((..((.((((((-..........)).)))).)-)..)))))(---((..(((.((....)).))).))).....(((((.....-------------------..))))).. ( -23.50)
>consensus
AAUCCGGUGACCUUGCACCU_CCAGUGUACCAGUGUGCCA_GCCCACCGC___CACCUCAUUGAACCCAUUGAAUGGAAUGCGACCCCUUUU___________________UCGGGUUUC
..(((((((....(((((......)))))...(((.((...)).)))......))))(((.((....)).)))..)))....(((((..........................))))).. (-17.24 = -17.90 +   0.67)

alignment

secondary structure

dotplot

Window 2

Location	5,293,815 – 5,293,935
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	78.57
Mean single sequence MFE	-34.65
Consensus MFE	-20.08
Energy contribution	-19.86
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-2.42
Structure conservation index	0.58
SVM decision value	1.03
SVM RNA-class probability	0.903081
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5293815 120 - 22224390
AAAAACCCAGAAAAAAAAUAGAAAAAAGAAAAGGGGUCGCAUUCCAUUCAAUGGAUUCAAUGAGGUGCAGGAGGUGGGCUUGGCACACUGCUAAACUGGAAGGUGCAAGGUCACCGGAUU
.....(((........................)))(((((((..((((.((....)).))))..))))....(((((.((((.(((.((.((.....)).))))))))).))))).))). ( -29.76)
>DroSec_CAF1 30964 94 - 1
GGAACCCGA-------------------AAAAGGGGUCGCAUUCCAUUCAAUGGGUUCAAUGAGGUG---GCGGUGGGC-UGGCACACUGGUACACAG---UGUGCAAGGUCACCGGAUU
.(((((((.-------------------.....(((......)))......))))))).........---.((((((.(-(.((((((((.....)))---))))).)).)))))).... ( -41.40)
>DroSim_CAF1 21748 96 - 1
GAAACCCGA-------------------AAAAGGGGUCGCAUUCCAUUCAAUGGGUUCAAUGAGGUG---GCGGUGGGC-UGGCACACUGGUACACUGG-AGGUGCAAGGUCACCGGAUU
....(((..-------------------....)))(((.....(((((((.((....)).))).)))---)((((((.(-(.((((.(..(....)..)-..)))).)).))))))))). ( -32.80)
>consensus
GAAACCCGA___________________AAAAGGGGUCGCAUUCCAUUCAAUGGGUUCAAUGAGGUG___GCGGUGGGC_UGGCACACUGGUACACUGG_AGGUGCAAGGUCACCGGAUU
.....((..........................(..((.((((......))))))..)..............(((((.(...((((................))))..).)))))))... (-20.08 = -19.86 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:53 2006